LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.14096 3.14096 3.14096 Created orthogonal box = (0 -41.6727 0) to (14.7324 41.6727 4.44199) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.35724 4.73518 4.44199 Created 178 atoms create_atoms CPU = 0.00018096 secs 178 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.35724 4.73518 4.44199 Created 178 atoms create_atoms CPU = 8.98838e-05 secs 178 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 3 15 1 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 11.5437 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 351 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 3 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.5437 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.918 | 4.918 | 4.918 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2197.3788 0 -2197.3788 88046.578 196 0 -2369.8463 0 -2369.8463 3858.2543 Loop time of 1.4063 on 1 procs for 196 steps with 351 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2197.37880505 -2369.84405529 -2369.84627145 Force two-norm initial, final = 360.549 0.300309 Force max component initial, final = 131.74 0.0955964 Final line search alpha, max atom move = 0.456181 0.0436093 Iterations, force evaluations = 196 369 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3638 | 1.3638 | 1.3638 | 0.0 | 96.98 Neigh | 0.022768 | 0.022768 | 0.022768 | 0.0 | 1.62 Comm | 0.014981 | 0.014981 | 0.014981 | 0.0 | 1.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004714 | | | 0.34 Nlocal: 351 ave 351 max 351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6543 ave 6543 max 6543 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 146190 ave 146190 max 146190 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146190 Ave neighs/atom = 416.496 Neighbor list builds = 7 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Setting up cg style minimization ... Unit style : metal Current step : 196 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.918 | 4.918 | 4.918 Mbytes Step Temp E_pair E_mol TotEng Press Volume 196 0 -2369.8463 0 -2369.8463 3858.2543 5454.2342 241 0 -2378.8157 0 -2378.8157 14399.034 5422.2969 Loop time of 0.229107 on 1 procs for 45 steps with 351 atoms 100.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2369.84627145 -2378.81506828 -2378.81565113 Force two-norm initial, final = 432.696 3.95512 Force max component initial, final = 338.542 2.97128 Final line search alpha, max atom move = 0.000482436 0.00143345 Iterations, force evaluations = 45 53 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22111 | 0.22111 | 0.22111 | 0.0 | 96.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020096 | 0.0020096 | 0.0020096 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005988 | | | 2.61 Nlocal: 351 ave 351 max 351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6543 ave 6543 max 6543 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 146158 ave 146158 max 146158 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146158 Ave neighs/atom = 416.405 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 3 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.5437 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.055 | 5.055 | 5.055 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2378.8157 0 -2378.8157 14399.034 Loop time of 2.14577e-06 on 1 procs for 0 steps with 351 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.146e-06 | | |100.00 Nlocal: 351 ave 351 max 351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6627 ave 6627 max 6627 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 145212 ave 145212 max 145212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 145212 Ave neighs/atom = 413.709 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.055 | 5.055 | 5.055 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -2378.8157 -2378.8157 14.294409 83.345443 4.5512975 14399.034 14399.034 851.84954 42086.358 258.89329 2.4736205 1719.0867 Loop time of 2.14577e-06 on 1 procs for 0 steps with 351 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.146e-06 | | |100.00 Nlocal: 351 ave 351 max 351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6627 ave 6627 max 6627 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 72606 ave 72606 max 72606 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 145212 ave 145212 max 145212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 145212 Ave neighs/atom = 413.709 Neighbor list builds = 0 Dangerous builds = 0 351 -2378.81565113437 eV 2.47362047599407 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01